Unlike the recent Spike.com rebrand, which saw video site IFILM.com folded into the network site, MTVN wants to keep the Atom and Comedy brands as separate entities while using the leverage they each have in their respective fields.

“The new Atom.com is our punk-rock label,” MTVN Entertainment Group executive vice president of digital media Erik Flannigan said at a press conference here Thursday. “It can tap into the power of Comedy Central, the brand and the network.”

In return, Comedy gets programming and talent. The network launched an Atom.com-branded program late Monday/early Tuesday at 2 a.m., and it already signed an on-air development deal with the creators of Atom.com original series Border Patrol.

Still, despite the crossover, there are no plans to syndicate Comedy content on Atom.com. While Comedy has been making its programming more widely available online, the need to differentiate the brands will mean that fans of The Daily Show with Jon Stewart and South Park will need to head to other sites (preferably Comedy’s own) to catch up on shows or segments they missed.

Nor is there any need to syndicate there, MTVN and Atom executives said, adding that Atomfilms.com drew 1.9 million unique visitors in May -- more than Funny or Die, The Onion and Super Deluxe combined.

Verizon Wireless was tapped as the launch sponsor, and it will use a new advertising system that largely does away with pre-rolls, instead wrapping ads around the content. Verizon will also sponsor the Atom-branded show on Comedy. The ability to sell ads in conjunction with the network was one of the reasons for aligning the channel with the short-form-video site.

The site is also shopping a series to potential advertisers called Agency, following a group of lazy office workers (ala The Office on NBC) working at an ad agency. The series would be developed with a sponsor in mind, and the advertising would become a part of the program, provided that the advertiser has a sense of humor about itself.

“The brand is the star of the show,” Flannigan said.

“Of course it has to work comedically,” added Comedy senior VP of programming and development Lou Wallach.

At launch, Atom.com will debut four new Web series: Border Patrol, which chronicles three slacker friends on lawn chairs monitoring the Mexican border; Steven & Stephen, from Tim Heidecker and Eric Wareheim of Adult Swim’s Tim and Eric Awesome Show, Great Job!; Stickman Exodus, which has stick figures come to life on the pages of a kid’s notebook; and Benny, Escaped Convict, co-created by Scrubs writer Ryan Levin, which follows a rodent on the lam.

Other shows under development include: Celebrity Bric a Brac by the creators of Web hit Chad Vader; Charlie’s Angels spoof McCaingels, which Atom said will be ready by the Republican National Convention; and a Legend of Zelda parody called Legend of Neil.

Users of the site will be able to upload their own material, with the best uploads featured in the “Showdown” section. If the video garners solid ratings from users, generates enough plays and catches the eye of Atom and Comedy staff, the uploader can gain “pro” status and will receive $500 toward future revenue sharing, as well as having their video appear on Atom TV.

Future plans include a video-on-demand channel, which Flannigan said is being targeted for a late-summer debut and, if Atom.com general manager Scott Roesch has his way, a shift in the time slot for Atom TV.

“We want a better time slot. We want bigger blocks of time,” Roesch said. “That day may come.”